Re: [galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'
On May 22, 2012, at 11:18 AM, Peter Cock wrote: > On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl wrote: >> Thanks Peter! It's very likely that I have the exact same problem, because I >> also have CentOS and needed to compile Python. > > In that case make sure you've done this: > > sudo yum install openssl openssl-dev > > and then repeat the Python 2.6 configure, make, make test, make install. > > Peter > > P.S. We also wanted this: > > sudo yum install bzip2 bzip2-devel > > At the end of the configure output you get told what Python modules > are disabled due to missing libraries - check this list for any other > potential problems later on. Hi Peter, Thanks for pointing this out, this information is useful and I've added it to "Step 0" at http://getgalaxy.org/ --nate > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl wrote: > Thanks Peter! It's very likely that I have the exact same problem, because I > also have CentOS and needed to compile Python. In that case make sure you've done this: sudo yum install openssl openssl-dev and then repeat the Python 2.6 configure, make, make test, make install. Peter P.S. We also wanted this: sudo yum install bzip2 bzip2-devel At the end of the configure output you get told what Python modules are disabled due to missing libraries - check this list for any other potential problems later on. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'
Thanks Peter! It's very likely that I have the exact same problem,
because I also have CentOS and needed to compile Python.
On 05/22/2012 05:04 PM, Peter Cock wrote:
On Tue, May 22, 2012 at 3:30 PM, Sarah Diehl wrote:
Hi all,
today I updated my test server to the newest galaxy-central version.
However, when I start it, I get the following error:
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 276, in command
relative_to=base, global_conf=vars)
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 313, in loadapp
**kw)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 413, in get_context
section)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit
value = import_string(found_expr)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in
from galaxy import config, jobs, util, tools
File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in
from galaxy.util.shed_util import *
File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in
from mercurial import ui, commands
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py",
line 12, in
import hg, scmutil, util, revlog, extensions, copies, error, bookmarks
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py",
line 12, in
import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo,
bookmarks
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py",
line 11, in
import changegroup, statichttprepo, error, httpconnection, url, util,
wireproto
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py",
line 11, in
import changelog, byterange, url, error
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py",
line 13, in
import httpconnection as httpconnectionmod
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py",
line 16, in
from mercurial import httpclient
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py",
line 48, in
import socketutil
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py",
line 82, in
class FakeSocket(httplib.FakeSocket):
AttributeError: 'module' object has no attribute 'FakeSocket'
Any help appreciated. Thanks.
Sarah
I had this happen to me last month,
https://twitter.com/#!/pjacock/statuses/194797125375234053
Quote: Just recompiled #Python 2.6 ... missing ssl libraries last time
finally bit me with import error doing 'from httplib import FakeSocket'
Basically (outside Galaxy), using the same Python that Galaxy
uses, try 'from httplib import FakeSocket' - if you get an ImportError
that explains why Galaxy breaks.
In my case this was a locally compiled Python (since we are using
CentOS where the system Python is too old), and we'd compiled
it without the SSL libraries. Until relatively recently this didn't
mater for using Galaxy - now it does.
Peter
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other G
Re: [galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'
On Tue, May 22, 2012 at 3:30 PM, Sarah Diehl wrote:
> Hi all,
>
> today I updated my test server to the newest galaxy-central version.
> However, when I start it, I get the following error:
>
> Traceback (most recent call last):
> File "./scripts/paster.py", line 34, in
> command.run()
> File
> "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 84, in run
> invoke(command, command_name, options, args[1:])
> File
> "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 123, in invoke
> exit_code = runner.run(args)
> File
> "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 218, in run
> result = self.command()
> File
> "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 276, in command
> relative_to=base, global_conf=vars)
> File
> "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 313, in loadapp
> **kw)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 204, in loadapp
> return loadobj(APP, uri, name=name, **kw)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 224, in loadobj
> global_conf=global_conf)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 248, in loadcontext
> global_conf=global_conf)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 278, in _loadconfig
> return loader.get_context(object_type, name, global_conf)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 413, in get_context
> section)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 458, in _context_from_explicit
> value = import_string(found_expr)
> File
> "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 18, in import_string
> return pkg_resources.EntryPoint.parse("x="+s).load(False)
> File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load
> entry = __import__(self.module_name, globals(),globals(), ['__name__'])
> File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in
> from galaxy import config, jobs, util, tools
> File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in
>
> from galaxy.util.shed_util import *
> File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in
>
> from mercurial import ui, commands
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py",
> line 12, in
> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py",
> line 12, in
> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo,
> bookmarks
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py",
> line 11, in
> import changegroup, statichttprepo, error, httpconnection, url, util,
> wireproto
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py",
> line 11, in
> import changelog, byterange, url, error
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py",
> line 13, in
> import httpconnection as httpconnectionmod
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py",
> line 16, in
> from mercurial import httpclient
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py",
> line 48, in
> import socketutil
> File
> "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py",
> line 82, in
> class FakeSocket(httplib.FakeSocket):
> AttributeError: 'module' object has no attribute 'FakeSocket'
>
>
> Any help appreciated. Thanks.
> Sarah
I had this happen to me last month,
https://twitter.com/#!/pjacock/statuses/194797125375234053
Quote: Just recompiled #Python 2.6 ... missing ssl libraries last time
finally bit me with import error doing 'from httplib import FakeSocket'
Basically (outside Galaxy), using the same Python that Galaxy
uses, try 'from httplib import FakeSocket' - if you get an ImportError
that explains why Galaxy breaks.
In my case this was a locally compiled Python (since we are using
CentOS where the system Python is too old), and we'd compiled
it without the SSL libraries. Until relatively recently this didn't
mater for using Galaxy - now it does.
Peter
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy
[galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'
Hi all,
today I updated my test server to the newest galaxy-central version.
However, when I start it, I get the following error:
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 276, in command
relative_to=base, global_conf=vars)
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 313, in loadapp
**kw)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 413, in get_context
section)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit
value = import_string(found_expr)
File
"/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in
from galaxy import config, jobs, util, tools
File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in
from galaxy.util.shed_util import *
File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in
from mercurial import ui, commands
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py",
line 12, in
import hg, scmutil, util, revlog, extensions, copies, error, bookmarks
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py",
line 12, in
import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo,
bookmarks
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py",
line 11, in
import changegroup, statichttprepo, error, httpconnection, url,
util, wireproto
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py",
line 11, in
import changelog, byterange, url, error
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py",
line 13, in
import httpconnection as httpconnectionmod
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py",
line 16, in
from mercurial import httpclient
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py",
line 48, in
import socketutil
File
"/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py",
line 82, in
class FakeSocket(httplib.FakeSocket):
AttributeError: 'module' object has no attribute 'FakeSocket'
Any help appreciated. Thanks.
Sarah
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
